Mercurial > repos > iuc > qiime_pick_open_reference_otus
annotate pick_open_reference_otus.xml @ 3:41482ca21d31 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
| author | iuc |
|---|---|
| date | Sat, 05 Aug 2017 07:24:40 -0400 |
| parents | f668a753bcfc |
| children | bf3348cc35d5 |
| rev | line source |
|---|---|
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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1 <tool id="qiime_pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0"> |
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3
41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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2 <description>(pick_open_reference_otus)</description> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff
changeset
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3 <macros> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff
changeset
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4 <import>macros.xml</import> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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5 </macros> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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6 <expand macro="requirements"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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7 <version_command>pick_open_reference_otus.py --version</version_command> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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8 <command detect_errors="aggressive"><![CDATA[ |
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3
41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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9 pick_open_reference_otus.py |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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10 --input_fps '$input_fps' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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11 -o otus |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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12 --otu_picking_method '$otu_picking_method' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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13 #if str( $ref_sequences.selector ) == 'history' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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14 #set $ref = $ref_sequences.reference_fp |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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changeset
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15 #else: |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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16 #set $ref = $ref_sequences.reference_fp.fields.path |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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changeset
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17 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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18 --reference_fp '$ref' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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changeset
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19 #if str( $prefilter.use_prefilter ) == 'yes' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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20 #if str( $prefilter.prefilter_ref_seq.selector ) == 'history' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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21 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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changeset
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22 #else: |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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23 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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24 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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25 --prefilter_refseqs_fp '$ref' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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26 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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27 --new_ref_set_id '$new_ref_set_id' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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28 $parallel |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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29 -O "\${GALAXY_SLOTS:-4}" |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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diff
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30 --percent_subsample '$percent_subsample' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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diff
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31 --prefilter_percent_id '$prefilter_percent_id' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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diff
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32 #if str($step1_otu_map_fp) != 'None': |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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33 --step1_otu_map_fp '$step1_otu_map_fp' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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34 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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diff
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35 #if str($step1_failures_fasta_fp) != 'None': |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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36 --step1_failures_fasta_fp='$step1_failures_fasta_fp' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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37 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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38 --minimum_failure_threshold '$minimum_failure_threshold' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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39 $suppress_step4 |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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40 --min_otu_size '$min_otu_size' |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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41 $suppress_taxonomy_assignment |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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42 $suppress_align_and_tree |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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43 |
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3
41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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44 #if str( $suppress_align_and_tree ) == "" |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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45 #if str( $suppress_taxonomy_assignment ) == "" |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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46 && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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47 && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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48 #else |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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49 && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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50 #end if |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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51 #end if |
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0
f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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52 ]]></command> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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53 <inputs> |
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3
41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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54 <param argument="--input_fps" type="data" format="fasta,fastq" multiple="true" label="Input sequence files"/> |
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0
f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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55 <param argument="--otu_picking_method" type="select" label="The OTU picking method to use for reference and de novo steps"> |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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56 <option value="uclust" selected="true">uclust</option> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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57 </param> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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58 <conditional name="ref_sequences"> |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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59 <param name="selector" type="select" label="Reference sequences to query"> |
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41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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60 <option value="cached" selected="true">Public databases</option> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 <option value="history">Databases from your history</option> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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62 </param> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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63 <when value="cached"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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64 <param argument="--reference_fp" label="Reference sequences" type="select"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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65 <options from_data_table="qiime_rep_set"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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66 </param> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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67 </when> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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68 <when value="history"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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69 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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70 </when> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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71 </conditional> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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72 <conditional name="prefilter"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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73 <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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74 <option value="true">True</option> |
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3
41482ca21d31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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75 <option value="false" selected="true">False</option> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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76 </param> |
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77 <when value="true"> |
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78 <conditional name="prefilter_ref_seq"> |
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79 <param name="selector" type="select" label="Reference sequences to query"> |
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80 <option value="cached" selected="true">Public databases</option> |
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0
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81 <option value="history">Databases from your history</option> |
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82 </param> |
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83 <when value="cached"> |
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84 <param argument="--prefilter_refseqs_fp" label="Reference sequences" type="select"> |
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85 <options from_data_table="qiime_rep_set"/> |
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86 </param> |
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87 </when> |
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88 <when value="history"> |
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89 <param argument="--prefilter_refseqs_fp" type="data" format="fasta" label="Reference databases"/> |
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90 </when> |
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91 </conditional> |
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92 </when> |
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93 <when value="false"/> |
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94 </conditional> |
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95 <param argument="--new_ref_set_id" type="text" value="New" label="Unique identifier for OTUs that get created in this ref set" help="This is useful to support combining of reference sets"/> |
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96 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/> |
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0
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97 <param argument="--percent_subsample" type="float" value="0.001" min="0" max="1" label="Percent of failure sequences to include in the subsample to cluster de novo" help="Large numbers should give more comprehensive results but will be slower"/> |
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98 <param argument="--prefilter_percent_id" type="float" value="0.0" min="0" max="1" label="Percent of sequence pre-cluster against the reference" help="Any reads which fail to hit are discarded (a quality filter)"/> |
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99 <param argument="--step1_otu_map_fp" type="data" format="txt" optional="true" label="Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional)" help="This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus"/> |
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100 <param argument="--step1_failures_fasta_fp" type="data" format="fasta" optional="true" label="Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional)" help="This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus"/> |
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101 <param argument="--minimum_failure_threshold" type="integer" value="100000" label="Minimum number of sequences that must fail to hit the reference for subsampling to be performed" help="If fewer than this number of sequences fail to hit the reference, the de novo clustering step will run serially rather than invoking the subsampled open reference approach to improve performance"/> |
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102 <param argument="--suppress_step4" type="boolean" truevalue="--suppress_step4" falsevalue="" checked="false" label="Suppress the final de novo OTU picking step?" help="It may be necessary for extremely large data sets"/> |
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103 <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU"/> |
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104 <param argument="--suppress_taxonomy_assignment" type="boolean" truevalue="--suppress_taxonomy_assignment" falsevalue="" checked="false" label="Skip the taxonomy assignment step?" help="It results in an OTU table without taxonomy"/> |
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105 <param argument="--suppress_align_and_tree" type="boolean" truevalue="--suppress_align_and_tree" falsevalue="" checked="false" label="Skip the sequence alignment and tree-building steps?"/> |
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0
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106 </inputs> |
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107 <outputs> |
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108 <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${tool.name} on ${on_string}: Final OTU map"/> |
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109 <data name="final_otu_map_mc" format="txt" from_work_dir="otus/final_otu_map_mc*.txt" label="${tool.name} on ${on_string}: Final OTU map without the OTUs failing the minimum specified OTU size"/> |
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110 <data name="rep_set" format="fasta" from_work_dir="otus/rep_set.fna" label="${tool.name} on ${on_string}: OTU representative sequences"/> |
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111 <data name="otu_table_mc" format="biom1" from_work_dir="otus/otu_table_mc*.biom" label="${tool.name} on ${on_string}: OTU table"/> |
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112 <data name="otu_table_mc_w_tax" format="biom1" from_work_dir="otus/otu_table_w_tax.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment"> |
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113 <filter>suppress_taxonomy_assignment is False</filter> |
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114 </data> |
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115 <data name="otu_table_mc_w_tax_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_w_tax_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment and without sequences failing the alignment to the OTU representative sequences"> |
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116 <filter>suppress_taxonomy_assignment is False and suppress_align_and_tree is False</filter> |
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117 </data> |
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118 <data name="otu_table_mc_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table without sequences failing the alignment to the OTU representative sequences"> |
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119 <filter>suppress_taxonomy_assignment is True and suppress_align_and_tree is False</filter> |
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120 </data> |
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121 <data name="rep_set_tree" format="txt" from_work_dir="otus/rep_set.tre" label="${tool.name} on ${on_string}: Representative set tree"> |
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122 <filter>suppress_align_and_tree is False</filter> |
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123 </data> |
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124 <data name="new_refseqs" format="fasta" from_work_dir="otus/new_refseqs.fna" label="${tool.name} on ${on_string}: New reference sequences (OTU + input reference sequences)"/> |
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125 </outputs> |
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126 <tests> |
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127 <test> |
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128 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/> |
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129 <param name="otu_picking_method" value="uclust"/> |
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130 <conditional name="ref_sequences"> |
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131 <param name="selector" value="history"/> |
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132 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/> |
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133 </conditional> |
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134 <conditional name="prefilter"> |
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135 <param name="use_prefilter" value="false"/> |
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136 </conditional> |
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137 <param name="new_ref_set_id" value="New"/> |
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138 <param name="parallel" value="--parallel"/> |
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139 <param name="percent_subsample" value="0.001"/> |
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140 <param name="prefilter_percent_id" value="0.0"/> |
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141 <param name="minimum_failure_threshold" value="100000"/> |
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142 <param name="suppress_step4" value=""/> |
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143 <param name="min_otu_size" value="2"/> |
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144 <param name="suppress_taxonomy_assignment" value=""/> |
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145 <param name="suppress_align_and_tree" value=""/> |
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146 <output name="final_otu_map" value="pick_open_reference_otus/1_final_otu_map.txt"/> |
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147 <output name="final_otu_map_mc" value="pick_open_reference_otus/1_final_otu_map_mc.txt"/> |
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148 <output name="rep_set"> |
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149 <assert_contents> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 <has_line line=">4374484 L1S8_76"></has_line> |
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151 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text> |
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152 </assert_contents> |
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153 </output> |
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154 <output name="rep_set_tree" value="pick_open_reference_otus/1_rep_set_tree.tre"/> |
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f668a753bcfc
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155 <output name="new_refseqs"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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157 <has_line line=">1109493"></has_line> |
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158 <has_text text=">945028"></has_text> |
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159 <has_text text=">4437874"></has_text> |
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160 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text> |
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161 </assert_contents> |
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162 </output> |
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163 </test> |
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164 <test> |
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165 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/> |
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f668a753bcfc
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166 <param name="otu_picking_method" value="uclust"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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167 <conditional name="ref_sequences"> |
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168 <param name="selector" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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169 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/> |
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f668a753bcfc
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170 </conditional> |
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171 <conditional name="prefilter"> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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172 <param name="use_prefilter" value="false"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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173 </conditional> |
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174 <param name="new_ref_set_id" value="New"/> |
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f668a753bcfc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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175 <param name="parallel" value="--parallel"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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176 <param name="percent_subsample" value="0.001"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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177 <param name="prefilter_percent_id" value="0.0"/> |
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178 <param name="minimum_failure_threshold" value="100000"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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179 <param name="suppress_step4" value=""/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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180 <param name="min_otu_size" value="3"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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181 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/> |
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182 <param name="suppress_align_and_tree" value="--suppress_align_and_tree"/> |
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f668a753bcfc
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183 <output name="final_otu_map" value="pick_open_reference_otus/2_final_otu_map.txt"/> |
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184 <output name="final_otu_map_mc" value="pick_open_reference_otus/2_final_otu_map_mc.txt"/> |
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185 <output name="rep_set"> |
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186 <assert_contents> |
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187 <has_line line=">4374484 L1S8_76"></has_line> |
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188 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text> |
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189 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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190 </output> |
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191 <output name="new_refseqs"> |
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192 <assert_contents> |
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193 <has_line line=">1109493"></has_line> |
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194 <has_text text=">945028"></has_text> |
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f668a753bcfc
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195 <has_text text=">4437874"></has_text> |
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f668a753bcfc
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196 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text> |
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197 </assert_contents> |
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198 </output> |
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199 </test> |
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200 <test> |
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201 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/> |
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202 <param name="otu_picking_method" value="uclust"/> |
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f668a753bcfc
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203 <conditional name="ref_sequences"> |
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204 <param name="selector" value="history"/> |
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205 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/> |
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206 </conditional> |
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207 <conditional name="prefilter"> |
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208 <param name="use_prefilter" value="false"/> |
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209 </conditional> |
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210 <param name="new_ref_set_id" value="New"/> |
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211 <param name="parallel" value="--parallel"/> |
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212 <param name="percent_subsample" value="0.001"/> |
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213 <param name="prefilter_percent_id" value="0.0"/> |
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214 <param name="minimum_failure_threshold" value="100000"/> |
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215 <param name="suppress_step4" value=""/> |
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216 <param name="min_otu_size" value="10"/> |
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217 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/> |
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218 <param name="suppress_align_and_tree" value=""/> |
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219 <output name="final_otu_map" value="pick_open_reference_otus/3_final_otu_map.txt"/> |
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220 <output name="final_otu_map_mc" value="pick_open_reference_otus/3_final_otu_map_mc.txt"/> |
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221 <output name="rep_set"> |
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222 <assert_contents> |
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223 <has_line line=">New.CleanUp.ReferenceOTU20 L1S8_4"></has_line> |
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224 <has_text text=">New.CleanUp.ReferenceOTU21 L1S140_45"></has_text> |
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225 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text> |
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226 </assert_contents> |
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227 </output> |
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228 <output name="rep_set_tree" value="pick_open_reference_otus/3_rep_set_tree.tre"/> |
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229 <output name="new_refseqs"> |
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230 <assert_contents> |
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231 <has_line line=">1109493"></has_line> |
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232 <has_text text=">945028"></has_text> |
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233 <has_text text=">4431138"></has_text> |
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234 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text> |
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235 </assert_contents> |
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236 </output> |
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237 </test> |
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238 </tests> |
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239 <help><![CDATA[ |
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240 **What it does** |
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241 |
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242 This tool performs open-reference OTU picking from sequences. |
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243 |
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244 This script is broken down into 4 possible OTU picking steps, and 2 steps |
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245 involving the creation of OTU tables and trees. |
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246 |
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247 More information about this tool is available on |
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248 `QIIME documentation <http://qiime.org/scripts/pick_open_reference_otus.html>`_. |
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249 ]]></help> |
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250 <citations> |
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251 <expand macro="citations"/> |
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252 </citations> |
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253 </tool> |